It's tough to point you in a good direction right now, because if I had it on my bench, I would just build you a new (well, new old stock) of that C4S board, pop it in, and mail the amp back to you. In your case, I would be tempted to have you take both C4S boards out and swap them between the amps. If the flashing board moves to the other amp, I can talk to the company ownership about kitting you up a replacement of that board and some parts to get you back on the road again. If the board doesn't flash in the other amp and the original problem stays put, then there's a connection issue underneath the board, or possibly one of the little zener diodes mounted on the 5 lug strip by the socket is acting up.
Perhaps the most sensible test is to put your meter negative probe into the black binding post so you don't have to hold it, hold your red meter probe into/against the metal tab of the MJE5731A transistor (should be Q2A) and observe the behavior when the amp starts. The voltage present there should pop up to around 375-400V, then settle down to just about dead nuts on at 350V. If that LED blinking and the noise is commensurate with the voltage on the MJE5731A tab dropping down to more like 300V, then popping back up, that is a good indicator that you just have a zener diode acting up.
Do also consider that swapping driver boards between amps could net you a pair of amps which both don't work, so I'd maybe start with the Q2A voltage measurements and keep the rest of this in the back of your mind for later.
